Methods for synthesizing a collection of partially identical polynucleotides

Abstract

Methods for synthesizing a collection of partially identical polynucleotides are disclosed.

1. A method for synthesizing a collection of partially identical polynucleotides, comprising:
 a) identifying a collection of unique, partially identical individual polynucleotide sequences to be synthesized; 
 b) analyzing the polynucleotide sequences with a phylogeny tree algorithm to make a phylogenetic tree; 
 c) identifying each individual branch group of the phylogenetic tree; 
 d) identifying each individual polynucleotide sequence in each individual branch group identified; 
 e) dividing each individual polynucleotide sequence in each branch group into smaller polynucleotide sequences; 
 f) identifying the smaller polynucleotide sequences common to all the individual polynucleotide sequences in each individual branch group identified if the branch group contains more than one individual polynucleotide sequence; 
 g) comparing the smaller polynucleotide sequences common to all the individual polynucleotide sequences in a first branch group with the smaller polynucleotide sequences from all other branch groups; 
 h) identifying the smaller polynucleotide sequences common to all branch groups; 
 i) identifying the smaller polynucleotide sequences common to only a subset of branch groups; 
 j) identifying the smaller polynucleotide sequences unique to each individual polynucleotide sequence in each branch group; 
 k) providing the smaller polynucleotide sequences of step h), step i), or step j) required to synthesize an individual polynucleotide sequence in a branch group; 
 l) synthesizing the individual partially identical polynucleotide sequence; and 
 m) repeating steps k) and l) until each individual polynucleotide sequence in the collection of partially identical polynucleotides is synthesized. 
 
     
     
       2. The method of  claim 1  wherein the smaller polynucleotide sequences are from 2 to 96 nucleotide residues in length. 
     
     
       3. The method of  claim 1  wherein the smaller polynucleotide sequences are 48 nucleotide residues in length. 
     
     
       4. The method of  claim 1  wherein the individual polynucleotide sequence is a double-stranded polynucleotide sequence.